We are creating new tools to diagnose infections in humans utilizing next
generation DNA sequencing combined with ultra-fast algorithms. Due to the
increased yield and ever decreasing costs of DNA sequencing we are now able to
inexpensively and efficiently find nucleic acids from microbes within normally
sterile human bio-fluids. We envision a $50 global assay for infectious agents
using this technology and we have concerted efforts to decrease the time to result.
Graduate students include: Kizee Etienne (fungal project), Angela Pena (viral
project) and Julliana Soto (bacterial project). MSc student include Pete Audano
(creator of K-analyze), Cai Huang (algorithm development), Shengyun Peng (k-
mer pipeline) and Vivek Sagar (creator of Clinical Metagenomics Analysis Pipeline
– CMAP). This work is in part funded by a generous Georgia Tech seed grant to our
group and Prof. King Jordan (Biology, Georgia Tech).

Human Genetics

Our laboratory is building an automated pipeline to analyze whole genome
datasets in the context defining the causative mutation underlying Mendelian
diseases. Recent work on a Mucopolysaccharidosis patient from Colombia revealed
a complex disorder intermediate between Sanfilippo and Hunter Syndromes.
We believe that whole genome sequencing will become the standard diagnostic
method for Mendelian disorders and by automating this pipeline we will be able
to enable a better understanding of the complex nature of the primary Mendelian
mutation as well as important genetic modifiers that can lead to differential clinical
presentation. Amit Rupani and Kelsey Rogowski have been leading these efforts.

We are also continuing our work on understanding the genetic basis of
susceptibility to infectious diseases, including work on Buruli ulcer in Ghana. Our
main collaborator is Prof. Julius Fobil at the University of Ghana.

Systems Biology

Nanovesicular exosomes are relatively understudied conveyers of action-at-a-
distance signaling within higher organisms. Swetha Srinivasan is carrying out
a systems biology approach to understand the role of these vesicles during the
immune response, especially focused on the role of Toll like receptor (TLR)
modulation of exosome composition and effector function. Pam Head, Jillian Le and
Michelle Su are undergraduate students who are contributing to various aspects the
research into the basic biology of exosomes. Andrew Sammond and Sean Lucking
are undergraduates who are investigating real time capture and visualization of
exosomes. This work is funded by a generous Georgia Tech seed grant to our group
in collaboration with Prof. Brandon Dixon (Mechanical Engineering , Georgia Tech).

Therapeutic decision analytics for cancer based upon DNA mutations and RNA
expression profiles will become the standard of care for cancer patients. Working
with Professor John McDonald’s laboratory (Georgia Tech), we are building a
computational pipeline to match mutations within a panel of cancer-linked genes
with optimal therapeutic strategy. Vivek Sagar and Benjamin Metcalf are leading
these studies within the laboratory. This work is funded by a generous grant from
the Cancer Treatment Centers of America.